GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cmutase in Pseudomonas stutzeri RCH2

Align Bifunctional chorismate mutase/prephenate dehydratase; Chorismate mutase-prephenate dehydratase; P-protein; EC 5.4.99.5; EC 4.2.1.51 (characterized)
to candidate GFF1941 Psest_1984 chorismate mutase domain of proteobacterial P-protein, clade 2

Query= SwissProt::P27603
         (365 letters)



>FitnessBrowser__psRCH2:GFF1941
          Length = 365

 Score =  690 bits (1780), Expect = 0.0
 Identities = 347/365 (95%), Positives = 357/365 (97%)

Query: 1   MSEADQLKALRVRIDSLDERILDLISERARCAQEVARVKTASWPKAEEAVFYRPEREAWV 60
           MS+ADQLKALRVRIDSLDERILDLISERARCAQEVARVKTA+  + E AVFYRPEREAWV
Sbjct: 1   MSDADQLKALRVRIDSLDERILDLISERARCAQEVARVKTAALAEGESAVFYRPEREAWV 60

Query: 61  LKHIMELNKGPLDNEEMARLFREIMSSCLALEQPLRVAYLGPEGTFSQAAALKHFGHSVI 120
           LKHIMELN+GPLDNEEMARLFREIMSSCLALEQPLRVAYLGPEGTFSQAAALKHFGH+VI
Sbjct: 61  LKHIMELNRGPLDNEEMARLFREIMSSCLALEQPLRVAYLGPEGTFSQAAALKHFGHAVI 120

Query: 121 SKPMAAIDEVFREVVAGAVNFGVVPVENSTEGAVNHTLDSFLEHDIVICGEVELRIHHHL 180
           S PMAAIDEVFREVVAGAVNFGVVPVENSTEGAVNHTLDSFLEHDIVICGEVELRIHHHL
Sbjct: 121 STPMAAIDEVFREVVAGAVNFGVVPVENSTEGAVNHTLDSFLEHDIVICGEVELRIHHHL 180

Query: 181 LVGETTKTDRITRIYSHAQSLAQCRKWLDAHYPNVERVAVSSNADAAKRVKSEWNSAAIA 240
           LVGETTKTDRITRIYSHAQSLAQCRKWLDAHYPNVERVAVSSNADAAKRVKSEWNSAAIA
Sbjct: 181 LVGETTKTDRITRIYSHAQSLAQCRKWLDAHYPNVERVAVSSNADAAKRVKSEWNSAAIA 240

Query: 241 GDMAAQLYGLSKLAEKIEDRPVNSTRFLIIGSQEVPPTGDDKTSIIVSMRNKPGALHELL 300
           GDMAAQLYGL+KLAEKIEDRP NSTRFLIIGSQEVPPTGDDKTSIIVSMRNKPGALHELL
Sbjct: 241 GDMAAQLYGLTKLAEKIEDRPDNSTRFLIIGSQEVPPTGDDKTSIIVSMRNKPGALHELL 300

Query: 301 MPFHSNGIDLTRIETRPSRSGKWTYVFFIDCMGHHQDPLIKNVLEKIGHEAVALKVLGSY 360
           +PFH+NGIDLTRIETRPSRSGKWTYVFFID +GHHQDPLIK+VLEKIG EAVALKVLGSY
Sbjct: 301 VPFHANGIDLTRIETRPSRSGKWTYVFFIDFLGHHQDPLIKDVLEKIGQEAVALKVLGSY 360

Query: 361 PKAVL 365
           PKAVL
Sbjct: 361 PKAVL 365


Lambda     K      H
   0.319    0.133    0.390 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 546
Number of extensions: 9
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 365
Length of database: 365
Length adjustment: 30
Effective length of query: 335
Effective length of database: 335
Effective search space:   112225
Effective search space used:   112225
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate GFF1941 Psest_1984 (chorismate mutase domain of proteobacterial P-protein, clade 2)
to HMM TIGR01807 (pheA: chorismate mutase (EC 5.4.99.5))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR01807.hmm
# target sequence database:        /tmp/gapView.21716.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01807  [M=76]
Accession:   TIGR01807
Description: CM_P2: chorismate mutase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
    7.1e-38  115.1   1.0    7.1e-38  115.1   1.0    1.9  2  lcl|FitnessBrowser__psRCH2:GFF1941  Psest_1984 chorismate mutase dom


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF1941  Psest_1984 chorismate mutase domain of proteobacterial P-protein, clade 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.1   1.0   7.1e-38   7.1e-38       1      76 []       7      85 ..       7      85 .. 0.96
   2 ?   -2.5   0.0      0.34      0.34      67      76 .]     126     135 ..     123     135 .. 0.80

  Alignments for each domain:
  == domain 1  score: 115.1 bits;  conditional E-value: 7.1e-38
                           TIGR01807  1 LkelRnkiDaiDdrildLlseRaklakavgelKkks...aseaviYRPeREaavlrrlkelnkGpLdqeavarifrE 74
                                        Lk+lR++iD++D+rildL+seRa++a++v+++K+++    + av+YRPeREa+vl++++eln+GpLd+e++ar+frE
  lcl|FitnessBrowser__psRCH2:GFF1941  7 LKALRVRIDSLDERILDLISERARCAQEVARVKTAAlaeGESAVFYRPEREAWVLKHIMELNRGPLDNEEMARLFRE 83
                                        799*******************************987666789********************************** PP

                           TIGR01807 75 im 76
                                        im
  lcl|FitnessBrowser__psRCH2:GFF1941 84 IM 85
                                        *9 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.34
                           TIGR01807  67 avarifrEim 76 
                                         a++ +frE++
  lcl|FitnessBrowser__psRCH2:GFF1941 126 AIDEVFREVV 135
                                         78999**995 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (76 nodes)
Target sequences:                          1  (365 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 1.58
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory